Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"Single-cell RNA sequencing offers opportunities to explore the depth of physiology, adaptation, and biochemistry in non-model organisms exposed to pollution","authors":"Reyna C. Collí-Dulá ,&nbsp;Irene Papatheodorou","doi":"10.1016/j.cbd.2024.101339","DOIUrl":"10.1016/j.cbd.2024.101339","url":null,"abstract":"<div><div>Single-cell Sequencing technology (scSeq) has revolutionized our understanding of individual cells, uncovering unprecedented heterogeneity within tissues and cell populations, principality through single-cell RNA Sequencing (scRNA-Seq). This short review highlights the pivotal role of scRNA-Seq in elucidating genotype-phenotype relationships, particularly in biological systems. Based on published articles, our analysis involved manual curation and automated Scopus tools to illustrate recent advances in the application of scRNA-Seq. The results reveal that scRNA-Seq has been extensively utilized in various biological areas, including biochemistry, genetics, molecular biology, immunology, and microbiology, followed by health sciences covering studies related to the nervous system, immune system, human health, development, and diseases, with a particular focus on cancer research. However, the potential of scRNA-Seq extends beyond disease research, offering insights into non-model organisms' responses to environmental contaminants. By enabling the study of cellular reactions at a molecular level, scRNA-Seq provides a comprehensive understanding of intracellular heterogeneity that enhances our comprehension of physiological, biochemical, and pathological environmental impacts on non-model organisms exposed to pollution. This understanding has many practical benefits, as it can aid in regulation and conservation efforts that benefit the environment and the use of economically essential and ecologically relevant organisms.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary Lithospermum erythrorhizon ethanol extract alleviates soybean meal-induced enteritis by improving immune tolerance profile of pearl gentian grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂)","authors":"Xin Lu,&nbsp;Yingrui Wu,&nbsp;Yinhui Peng,&nbsp;Kianann Tan,&nbsp;Ming Liu,&nbsp;Xueying Liang,&nbsp;Peng Xu,&nbsp;Mingzhong Liang,&nbsp;Wenjie Liu,&nbsp;Qingfang Gong,&nbsp;Xiaohui Cai","doi":"10.1016/j.cbd.2024.101335","DOIUrl":"10.1016/j.cbd.2024.101335","url":null,"abstract":"<div><div>The aquaculture industry has a shortage of objected protection against soybean meal-induced enteritis (SBMIE) in carnivorous fish caused by soybean meal feed. Our initial study discovered that <em>Lithospermum erythrorhizon</em> (LE) ethanol extract has potential application value in improving SBMIE. A feeding trial (for eight weeks) was conducted to investigate LE ethanol extract on pearl gentian grouper SBMIE of protection to clarify the influence of LE ethanol extract on the immune tolerance profile. Three hundred and sixty pearl gentian groupers were administered one of three distinct dietary regimes: 1) 100 % fish meal (FM); 2) soybean meal substitution of 50 % fish meal protein (SBM); 3) SBM diet +0.2 % LE ethanol extract (SBMLE). Each treatment included three 1000 L cisterns—each of cisterns with 30 fish. The preliminary weight of the fish varied between 72.01 g and 72.50 g. Growth performance results showed that WGR and SGR were significantly decreased in the SBM group (<em>P</em> &lt; 0.05), while there was no significant difference between the FM and SBMLE groups. There was no significant difference in survival among the three groups. The results showed that SBM-fed fish exhibited enteritis manifested by mucosal fold shortening, lamina propria widening, decreased serum immune markers (IgM, C3, and C4), and up-regulated expression of pro-inflammatory cytokines (<em>il17</em> and <em>il12</em>) and immune-related gene (<em>tlr3</em>, and <em>tlr9</em>). The addition of 0.2 % LE ethanol extract to the SBM diet, reversed the above symptoms, and anti-inflammatory cytokine (<em>tgf-β1</em>), gene expression increased significantly (<em>P</em> &lt; 0.05). Intestinal transcriptome analysis exhibited that the DEGs between the FM group and the SBM group were mainly enriched in FoxO signaling pathway, while the DEGs between the SBM group and the SBMLE group were enriched in MAPK signaling pathway and FoxO signaling pathway. The RT-qPCR results also revealed changes in MAPK/FoxO signaling pathway-related genes, including <em>Dusp1</em>, <em>jund</em>, <em>Irs2b</em>, <em>fbxo32</em>, and <em>ccng2</em>. Overall, <em>Lithospermum erythrorhizon</em> ethanol extract may alleviate SBMIE by regulating MAPK/FoxO signaling pathway, which would be beneficial for enhancing the immune tolerance and utilization efficiency of pearl gentian groupers to dietary soybean meal.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142442910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-organ transcriptomics analysis of a slowly growing fish rock carp (Procypris rabaudi) reveals insights into mechanism of growth rate regulation","authors":"Hongsen Lv ,&nbsp;Anxiang Wang ,&nbsp;Jingning Ling ,&nbsp;Yixiao Li ,&nbsp;Yuanfa He ,&nbsp;Hui Luo ,&nbsp;Hua Ye ,&nbsp;Weizhi Yao ,&nbsp;Shengqi Su ,&nbsp;Wenping He","doi":"10.1016/j.cbd.2024.101337","DOIUrl":"10.1016/j.cbd.2024.101337","url":null,"abstract":"<div><div>To explore the patterns of differentially expressed genes (DEGs) associated with different growth rates in rock carp (<em>Procypris rabaudi</em>), transcriptome sequencing was performed on the muscle, liver, and brain tissues of rock carp. Subsequently, bioinformatics analysis was conducted, and 2129, 1380, and 415 DEGs were identified in the muscle, liver, and brain tissues, respectively. GO enrichment and KEGG pathway analysis revealed that genes related to appetite regulation, protein degradation and digestion, lipid transport and metabolisms, and glycolysis/gluconeogenesis were upregulated in individuals with slower growth rates. Differential expression analysis identified 21 genes associated with feeding and metabolism across three tissues, including <em>mc4r</em>, <em>npy</em>, and <em>npry</em> in brain tissue; <em>fatp</em>, <em>fabp</em>, <em>pparα</em>, and <em>apo</em> in liver tissue; and <em>prss</em>, <em>ctrl</em>, and <em>cela</em> in muscle tissue. All these genes were upregulated in the slow-growing fish. Furthermore, weighted gene co-expression network analyses, including three modules (yellow, turquoise, and brown), significantly associated with growth. A network map that included these three modules enabled the identification of a series of hub genes, including <em>rp13a</em>, <em>ube2o</em>, <em>h6pd</em>, etc. These genes may be key candidate genes regulating the growth of rock carp. This study contributes to a deeper understanding of the growth control mechanism in rock carp and offers a scientific basis for efficient breeding and species improvement.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142446791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of key lncRNAs and mRNAs in muscle development pathways of Tan sheep","authors":"Jiawei Lu,&nbsp;Yilan Liu,&nbsp;Huixia Li","doi":"10.1016/j.cbd.2024.101336","DOIUrl":"10.1016/j.cbd.2024.101336","url":null,"abstract":"<div><div>The study aimed to identify the long noncoding RNA (lncRNA) responsible for regulating muscle development in Tan sheep. RNA-seq analysis was conducted on <em>longissimus dorsi</em> samples from 1-day-old and 60-day-old Tan sheep to investigate the molecular processes involved in muscle development. A total of 5517 lncRNAs and 2885 mRNAs were found to be differentially expressed in the 60-day-old Tan sheep. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these differentially expressed lncRNAs and mRNAs were linked to pathways crucial for muscle development, such as MAPK, cAMP, and calcium-mediated signaling pathways. Key genes like <em>CDKN1A</em>, <em>MAPK14</em>, <em>TGFB1</em>, <em>MEF2C</em>, <em>MYOD1</em>, and <em>CD53</em> were identified as significant players in muscle development. The study validated the RNA-seq results through RT-qPCR, confirming the consistency of expression levels of differentially expressed lncRNAs and mRNAs. These findings indicate that lncRNA-mRNA networks produce a remarked effect on modulating muscle development in Tan sheep, such as lncRNAs (MSTRG.12808.1/MSTRG.22662.3/MSTRG.18310.1) and mRNAs (<em>MSTRG.10027</em>/<em>MSTRG.10029</em>/<em>MSTRG.10258</em>/<em>MSTRG.11011</em>/<em>MSTRG.10354</em>), laying the groundwork for future research in this area.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chronic thermal stress on Octopus maya embryos down-regulates epigenome-related genes and those involved in the nervous system development and morphogenesis","authors":"Pavel Galindo-Torres ,&nbsp;Carlos Rosas ,&nbsp;Sadot Ramos-Rodríguez ,&nbsp;Clara E. Galindo-Sánchez","doi":"10.1016/j.cbd.2024.101332","DOIUrl":"10.1016/j.cbd.2024.101332","url":null,"abstract":"<div><div>Red <em>Octopus maya</em> is strongly influenced by temperature. Recent studies have reported negative reproduction effects on males and females when exposed to temperatures higher than 27 °C. Embryos under thermal stress show morphological and physiological alterations; similar phenotypes have been reported in embryos from stressed females, evidencing transgenerational consequences. Transcriptomic profiles were characterized along embryo development during normal-under thermal stress and epigenetic alterations through DNA methylation and damage quantification. Total RNA in organogenesis, activation, and growth stages in control and thermal stress were sequenced with Illumina RNA-Seq. Similarly, total DNA was used for DNA methylation and damage quantification between temperatures and embryo stages. Differential gene expression analyses showed that embryos express genes associated with oxygen transport, morphogenesis, nervous system, neuroendocrine cell differentiation, spermatogenesis, and male sex differentiation. Conversely, embryos turn off genes involved mainly in nervous system development, morphogenesis, and gene expression regulation when exposed to thermal stress – consistent with <em>O. maya</em> embryo phenotypes showing abnormal arms, eyes, and body development. No significant differences were observed in quantifying DNA methylation between temperatures but they were for DNA damage quantification. Epigenetic alterations are hypothesized to occur since several genes found downregulated belong to the epigenetic machinery but at histone tail level.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142376469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis elucidates mating affects the expression of intra-/extra-ovarian factors, thereby influencing ovarian development in the mud crab Scylla paramamosain","authors":"Li Benzhen,&nbsp;Shao Shucheng,&nbsp;Bao Chenchang,&nbsp;Cui Zhaoxia,&nbsp;Yang Yanan","doi":"10.1016/j.cbd.2024.101334","DOIUrl":"10.1016/j.cbd.2024.101334","url":null,"abstract":"<div><div>Prior to the pubertal molt and mating, the ovarian development of the mud crab <em>Scylla paramamosain</em> was primarily at stage II. However, immediately after mating, female crabs initiate vitellogenesis, and their ovaries quickly develop. The aim of this study was to identify differentially expressed genes associated with ovarian development in the mud crab before and after mating, in order to elucidate the influence of mating on ovarian development using comparative transcriptomics. The KEGG pathway analysis results indicated that ribosome and ribosome-related pathways were highly associated with ovarian development at stage II across both transcriptomes, likely to support the subsequent vitellogenesis by providing the necessary materials. Additionally, the neurodegeneration, MAPK, cAMP and PLD pathways were active in regulating oogonia differentiation, oocyte proliferation and vitellogenesis after mating. Meanwhile, certain intra-ovarian factors, such as the cell cycle-related genes cyclin B and APC, the forkhead box family genes Foxl2 and slp1, the SOX family gene SOX5-like, the hormone-related genes SULT1E1 and Eip74EF-like, the growth factor-related genes VEGFD-like and CUBE1-like, as well as HPS10 and tra1-like, have essential functions in regulating ovarian development after mating. Furthermore, the receptors of extra-ovarian hormones, such as RPCHR, HR4, and ILR1, as well as the neurotransmitter receptor 5-HTR4, were involved in ovarian development. It is believed that ovarian development is controlled by the coordinated action of both intrinsic and extrinsic endocrine factors, and these factors are influenced by mating. Finally, the analysis of epigenic modification-related genes, transcription factors, and target genes revealed the regulation of gene expression. Our study indicated that, those genes work in a coordinated manner to regulate the complex processes of follicle cell development, oogonia differentiation, oocyte proliferation, and vitellogenesis during ovarian development.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analyses of the transcriptome among three development stages of Zeugodacus tau larvae (Diptera: Tephritidae)","authors":"Wei-Jun Li ,&nbsp;Cui-Kang Xu ,&nbsp;Song-Quan Ong ,&nbsp;Abdul Hafiz Ab Majid ,&nbsp;Jian-Guo Wang ,&nbsp;Xiao-Zhen Li","doi":"10.1016/j.cbd.2024.101333","DOIUrl":"10.1016/j.cbd.2024.101333","url":null,"abstract":"<div><div>Studying differences in transcriptomes across various development stages of insects is necessary to uncover the physiological and molecular mechanism underlying development and metamorphosis. We here present the first transcriptome data generated under Illumina Hiseq platform concerning <em>Zeugodacus tau</em> (Walker) larvae from Nanchang, China. In total, 11,702 genes were identified from 9 transcriptome libraries of three development stages of <em>Z. tau</em> larvae. 7219 differentially expressed genes (DEGs) were screened out from the comparisons between each two development stages of <em>Z. tau</em> larvae, and their roles in development and metabolism were analyzed. Comparative analyses of transcriptome data showed that there are 5333 DEGs between 1-day and 7-day old larvae, consisting of 1609 up-regulated and 3724 down-regulated genes. Expressions of DEGs were more abundant in L7 than in L1 and L3, which might be associated with metamorphosis. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested the enrichment of metabolic process. KOG annotation further confirmed that 20-hydroxyecdysone (20E) pathway related genes <em>Cyp4ac1_1</em>, <em>Cyp4aa1</em>, <em>Cyp313a4_3</em> were critical for the biosynthesis, transport, and catabolism of secondary metabolites and lipid transport and metabolism. Expression patterns of 8 DEGs were verified using quantitative real-time PCR (RT-qPCR). This study elucidated the DEGs and their roles underlying three development stages of <em>Z. tau</em> larvae, which provided valuable information for further functional genomic research.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis-based study on the response mechanism of juvenile golden cuttlefish (Sepia esculenta) to benzo[a]pyrene exposure","authors":"Fei Han,&nbsp;Xiaodong Zheng","doi":"10.1016/j.cbd.2024.101331","DOIUrl":"10.1016/j.cbd.2024.101331","url":null,"abstract":"<div><p>Benzo[<em>a</em>]pyrene (BaP), a polycyclic aromatic hydrocarbon from incomplete combustion, builds up in coastal regions through river runoff, atmospheric deposition, and coastal activities. BaP's lipophilicity and stability lead to persistent environmental impacts due to its resistance to degradation. The economically valuable golden cuttlefish, <em>Sepia esculenta</em>, often spawns and hatches in shallow waters, making it prone to BaP exposure. This study employs transcriptomic analysis to initially investigate juvenile golden cuttlefish's response to BaP. The results indicate that BaP exposure significantly affects various physiological and molecular functions of the juveniles, particularly affecting pathways related to immune and inflammatory responses, metabolic regulation, and nervous system functions. Functional enrichment and PPI network analyses identified key genes such as HSGALT-like, ASAH1-like, and GTL-like in the BaP response. These genes exhibited a suppressive trend during short-term exposure, indicating that BaP exposure may influence lipid metabolism, energy conversion, and digestive functions at the genetic level, which could further disrupt the overall physiological state and developmental processes of juvenile golden cuttlefish. The study offers novel insights into BaP's effects on juvenile golden cuttlefish and marine life, aiding marine ecosystem and biodiversity conservation.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive transcriptome analysis unravels the perturbated cardiovascular-related molecular mechanisms of tilapia under high-temperature stress","authors":"Jigang Lu ,&nbsp;Yihao Zhu ,&nbsp;Shicen Wei ,&nbsp;Siqi Huang ,&nbsp;Yao Zu ,&nbsp;Liangbiao Chen","doi":"10.1016/j.cbd.2024.101324","DOIUrl":"10.1016/j.cbd.2024.101324","url":null,"abstract":"<div><p>With the ongoing intensification of global warming, thermal stress poses significant challenges to tilapia aquaculture. However, the molecular mechanisms underlying the cardiac response of tilapia to high temperatures remain largely unexplored. To address this knowledge gap, we investigated the effects of high-temperature stress on the transcriptomic landscape of the tilapia heart. RNA sequencing was performed on the hearts of <em>Oreochromis aureus</em> (AR), <em>Oreochromis niloticus</em> (NL), and hybrids (<em>O. niloticus</em> ♀ × <em>O. aureus</em> ♂, AN) under treatments of 28 °C, 36 °C, and 39 °C. Using a multi-method approach, including Differentially Expressed Genes analysis, Weighted Gene Co-expression Network Analysis, Fuzzy C-Means, Self-Organizing Map, and Support Vector Machine-Recursive Feature Elimination, we identified six marker genes at 39 °C (AR: <em>ptges3</em>, <em>tuba1a</em>; NL: <em>ran</em>, <em>tcima</em>; AN: <em>slc16a1</em>, <em>fam184b</em>). These genes exhibited strong positive correlations and increased expression under high-temperature conditions. Gene Set Enrichment Analysis and GENIE3 revealed that these marker genes closely regulate three cardiovascular-related pathways: adrenergic signaling in cardiomyocytes, vascular smooth muscle contraction, and cardiac muscle contraction. We hypothesize that the synergistic inhibition of these pathways by marker genes leads to the deterioration of cardiovascular function. In summary, thermal stress activates marker genes, which in turn inhibit cardiovascular pathways, impairing cardiac performance. We propose that these marker genes could serve as dynamic thermal indicators of cardiac performance in tilapia. Additionally, our findings provide theoretical support for improving the management of tilapia farming under high-temperature stress.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142240490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes","authors":"Chunxi Jiang,&nbsp;Hongsheng Yang,&nbsp;Bohong Liu,&nbsp;Lina Sun","doi":"10.1016/j.cbd.2024.101328","DOIUrl":"10.1016/j.cbd.2024.101328","url":null,"abstract":"<div><p>Sea cucumbers, marine benthic invertebrates, play crucial roles in maintaining the stability of marine ecosystems and hold key evolutionary positions. However, information regarding their genomes remains limited. Here, we conducted genome survey analyses on seven species from four orders. Results indicated that <em>Colochirus anceps</em>, <em>Colochirus quadrangularis</em>, and <em>Pseudocolochirus violaceus</em> within the order Dendrochirotida have significantly larger genomes (2238–3754 Mbp) compared to conventional sea cucumber genomes, accompanied by a very high proportion of repeat sequences (69.39–72.52 %). While <em>Holothuria edulis</em> and <em>Holothuria atra</em> exhibited similar genome sizes comparable to those of other species within the order Holothuriida, heterozygosity and repeat content varied among all the six species in this order. The representative species <em>Apostichopus californicus</em> of the order Synallactida possesses the smallest genome size (573.45Mbp) within its order, but its heterozygosity (2.24 %) is significantly higher than that of other species. The representative species <em>Synapta maculata</em> of the order Apodida exhibited a normal genome size (900.97 Mbp), lower proportion of repeat sequences (42.19 %), and lower heterozygosity (0.84 %), making it the species with the least challenges for genome sequencing and assembly in the future among all surveyed species. Subsequently, we compiled genomic information from a total of 19 sea cucumber genomes, both newly sequenced and previously reported, revealing a significant linear relationship (<em>P</em> = 0.0001) between genome size and the proportion of repeat sequences in sea cucumbers. Additionally, phylogenetic and comparative analysis of mitochondrial genomes among them indicated extensive rearrangements within the order Apodida, leading to significant discrepancies between mitochondrial and nuclear genome phylogenies.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}